Refined Models for Indels

[Rob-Schuetz]

Hello,

Do you have trained indel models available that return refined genotype predictions? When I pass model_type="Refine" and model_trained="insertions_250x.RF.rds" to Prediction.r, only Phase prediction is returned rather than refined genotype prediction.

Figure 3c-d in your paper (https://www.nature.com/articles/s41587-019-0368-8) shows refined genotype results for indels, and I'm curious as to which trained models were used to obtain these results.

Thanks, Rob

[douym]

Hello,

Do you have trained indel models available that return refined genotype predictions? When I pass model_type="Refine" and model_trained="insertions_250x.RF.rds" to Prediction.r, only Phase prediction is returned rather than refined genotype prediction.

Figure 3c-d in your paper (https://www.nature.com/articles/s41587-019-0368-8) shows refined genotype results for indels, and I'm curious as to which trained models were used to obtain these results.

Thanks, Rob

Hi Rob,

Thanks for your interest in using MosaicForecast! Unfortunately I have not trained Refine model for indels, since there are too few experimentally-evaluated phasable indels in our dataset to correct that.

Best wishes,

Yanmei

[Rob-Schuetz]

Hi Yanmei,

I see, thank you for getting back to me. The phasing model should work just fine, I was just interested.

Thanks, Rob